Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9319	0.61
27DAP/17DAP	1.30919	0.849
39DAP/27DAP	1.19226	0.572
41DAP/39DAP	1.22647	0.914
42DAP/41DAP	1.46501	0.441
43DAP/42DAP	0.95008	0.877
47DAP/43DAP	0.93615	0.754
52DAP/47DAP	1.18417	0.886
57DAP/52DAP	1.22886	0.927

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95231	0.39
17DAP/reference	1.17376	0.061
27DAP/reference	1.09191	0.152
39DAP/reference	1.19894	0.047
41DAP/reference	1.0739	0.203
42DAP/reference	0.91176	0.12
43DAP/reference	1.03731	0.617
47DAP/reference	1.01931	1
52DAP/reference	0.86889	0.084
57DAP/reference	1.02074	0.901

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42206	0.081
27DAP/17DAP	1.09651	0.751
39DAP/27DAP	0.94731	0.747
41DAP/39DAP	1.0261	1
42DAP/41DAP	1.13738	0.478
43DAP/42DAP	0.97264	0.801
47DAP/43DAP	1.13084	0.865
52DAP/47DAP	1.11633	0.689
57DAP/52DAP	1.00569	0.869
57DAP/7DAP	0.98548	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97226	0.55
17DAP/reference	0.9602	0.447
27DAP/reference	0.99538	0.698
39DAP/reference	1.04189	1
41DAP/reference	0.96697	0.489
42DAP/reference	1.09863	0.686
43DAP/reference	1.14515	0.111
47DAP/reference	1.03362	0.948
52DAP/reference	1.1576	0.266
57DAP/reference	1.19191	0.214

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05329	0.679
17DAP/reference	1.1184	0.375
27DAP/reference	1.10997	0.412
39DAP/reference	0.97637	0.485
41DAP/reference	0.99435	0.57
42DAP/reference	0.85969	0.019
43DAP/reference	1.36742	0.023
47DAP/reference	1.01596	0.79
52DAP/reference	0.95514	0.327
57DAP/reference	1.07998	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76319	0.037
17DAP/reference	0.94044	0.364
27DAP/reference	1.20658	0.085
39DAP/reference	1.02196	1
41DAP/reference	1.08774	0.471
42DAP/reference	1.0641	0.635
43DAP/reference	1.00443	0.858
47DAP/reference	0.95922	0.434
52DAP/reference	1.08247	0.649
57DAP/reference	0.89356	0.174

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24054	0.966
26DAP/20DAP	1.58447	0.099
34DAP/26DAP	0.87641	0.61
51DAP/34DAP	0.77823	0.109
52DAP/51DAP	1.17477	0.481
53DAP/52DAP	1.11783	1
55DAP/53DAP	0.76447	0.336
57DAP/55DAP	1.20682	0.818
62DAP/57DAP	1.12187	0.8
68DAP/62DAP	1.16598	1
68DAP/14DAP	0.86667	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.45442	0.029

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.4313	0.058
Mature Green Tomato/Ripe Tomato	1.17575	0.774
Immature Eggplant/Mature Eggplant	2.02751	0.05
Ripe Pepper/Ripe Tomato	0.44741	0.224
Mature Eggplant/Ripe Tomato	0.9248	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05484
1-1-2/M82	1.06989	1
12-2/M82	N/A	N/A
12-4/M82	1.01301	1
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.77275
3-2/M82	1.42934
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.17577	1
5-3/M82	0.85235	1
6-2/M82	0.87007
6-3/M82	N/A	N/A
7-1/M82	0.99577
7-2/M82	1.12606	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.39886	0.277
IL2-6/WTpooled	0.59597	0.348
IL7-5/WTpooled	1.12136	0.75
IL7-3/WTpooled	1.0659	1
IL12-4/WTpooled	1.22957	0.695
IL1-4/WTpooled	1.00828
WT/WTpooled	1.0726	0.911

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.90602	0.256

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05451	0.758
DC3000/delta hrp 6h	1.12754	1
DC3000/delta hrp 12h	0.94804	1
DC3000/delta hrp 24h	1.06396	0.604

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02548	1
DC3000 delta B/DC3000 delta AB	0.97132

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00348	1
Exp 36h	1.76616	0.693
Exp 60h	1.554	0.399

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.03859	1
Var 0h	0.96515	1
Var 12h I row2-row1	1.25225	0.222
Var 12h NI row2-row1	1.16834	0.649
Var 36h I row2-row1	0.88804	1
Var 36h NI row2-row1	0.98906	0.791
Var 60h I row2-row1	0.90091	0.582
Var 60h NI row2-row1	1.16753	0.904
Time course 0hI-0hNI	0.96763	0.843
Time course 12hI-12hNI	1.18054	0.077
Time course 36hI-36hNI	1.19307	0.044
Time course 60hI-60hNI	1.41641	0.009

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.91086	0.348
transgenic ySAMdc/azygous control (breaker)	0.79234	0.251
transgenic ySAMdc/azygous control (red)	0.89629	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98625	0.5

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.93985	0.308

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85736	0.172
Manapal/WT (break)	0.70186	0.333
Manapal/WT (red)	0.8975	0.315